Starting phenix.real_space_refine on Sat Jun 21 02:21:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yhs_33837/06_2025/7yhs_33837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yhs_33837/06_2025/7yhs_33837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yhs_33837/06_2025/7yhs_33837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yhs_33837/06_2025/7yhs_33837.map" model { file = "/net/cci-nas-00/data/ceres_data/7yhs_33837/06_2025/7yhs_33837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yhs_33837/06_2025/7yhs_33837.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 108 5.49 5 S 25 5.16 5 C 15076 2.51 5 N 4520 2.21 5 O 4867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24596 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3039 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 24, 'TRANS': 398} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 377 Unresolved non-hydrogen angles: 480 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 12, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 256 Chain: "C" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2240 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 12, 'TRANS': 311} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "E" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2548 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2529 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "H" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2490 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2514 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 1 Chain: "L" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1428 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "M" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1226 Classifications: {'RNA': 58} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 18, 'rna3p_pur': 14, 'rna3p_pyr': 13} Link IDs: {'rna2p': 29, 'rna3p': 28} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 803 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "O" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 244 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 14.35, per 1000 atoms: 0.58 Number of scatterers: 24596 At special positions: 0 Unit cell: (148.41, 138.71, 181.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 108 15.00 O 4867 8.00 N 4520 7.00 C 15076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.09 Conformation dependent library (CDL) restraints added in 3.0 seconds 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5482 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 40 sheets defined 30.7% alpha, 17.8% beta 31 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 8.77 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 removed outlier: 4.159A pdb=" N PHE A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 removed outlier: 4.325A pdb=" N LEU A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.083A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.752A pdb=" N GLN A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 162 removed outlier: 3.625A pdb=" N ARG A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.554A pdb=" N ALA A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.896A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.668A pdb=" N LEU A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 3.731A pdb=" N ILE A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.842A pdb=" N TRP A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 374 through 382 removed outlier: 4.174A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.753A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.912A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 148 removed outlier: 3.596A pdb=" N ARG C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.727A pdb=" N ARG C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.571A pdb=" N ALA C 174 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 223 Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.658A pdb=" N ILE C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 339 through 352 Processing helix chain 'D' and resid 130 through 148 removed outlier: 3.849A pdb=" N ARG D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 208 through 223 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.734A pdb=" N ILE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 33 through 48 removed outlier: 3.902A pdb=" N PHE E 37 " --> pdb=" O SER E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 135 removed outlier: 3.508A pdb=" N GLY E 135 " --> pdb=" O GLN E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.954A pdb=" N LEU E 193 " --> pdb=" O ARG E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 removed outlier: 3.617A pdb=" N ALA E 212 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 removed outlier: 3.734A pdb=" N ARG F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.646A pdb=" N ARG F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 224 Processing helix chain 'F' and resid 275 through 284 removed outlier: 3.603A pdb=" N ILE F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 331 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.536A pdb=" N SER G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 293 through 297 removed outlier: 3.786A pdb=" N LEU G 296 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY G 297 " --> pdb=" O ASP G 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 293 through 297' Processing helix chain 'G' and resid 322 through 331 removed outlier: 3.631A pdb=" N LEU G 326 " --> pdb=" O ASP G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 86 through 91 removed outlier: 3.911A pdb=" N ILE H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 224 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 92 removed outlier: 3.675A pdb=" N LEU I 86 " --> pdb=" O ASP I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 148 removed outlier: 3.772A pdb=" N ARG I 134 " --> pdb=" O ASP I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 163 Processing helix chain 'I' and resid 208 through 222 Processing helix chain 'I' and resid 275 through 283 removed outlier: 3.658A pdb=" N ILE I 279 " --> pdb=" O HIS I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 297 removed outlier: 3.535A pdb=" N LEU I 296 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY I 297 " --> pdb=" O ASP I 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 293 through 297' Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 removed outlier: 3.577A pdb=" N GLN I 342 " --> pdb=" O ALA I 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 14 removed outlier: 4.116A pdb=" N TYR J 12 " --> pdb=" O ASP J 8 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN J 14 " --> pdb=" O ASP J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 78 Processing helix chain 'J' and resid 79 through 100 removed outlier: 3.659A pdb=" N VAL J 83 " --> pdb=" O ARG J 79 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 27 Processing helix chain 'L' and resid 108 through 118 removed outlier: 4.474A pdb=" N LEU L 112 " --> pdb=" O ASN L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.432A pdb=" N ALA A 191 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ASN E 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.432A pdb=" N ALA A 191 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ASN E 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE E 279 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA E 257 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU E 281 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR E 255 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU E 283 " --> pdb=" O ALA E 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA5, first strand: chain 'C' and resid 31 through 33 Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 45 removed outlier: 4.285A pdb=" N VAL C 228 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU C 229 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 176 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG C 191 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 43 through 45 removed outlier: 4.285A pdb=" N VAL C 228 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU C 229 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 176 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA9, first strand: chain 'D' and resid 127 through 128 removed outlier: 4.044A pdb=" N ALA D 127 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AB2, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.878A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 184 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA D 176 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG D 191 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 63 through 70 Processing sheet with id=AB4, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.737A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 56 through 61 removed outlier: 5.411A pdb=" N GLY E 58 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 110 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 56 through 61 removed outlier: 5.411A pdb=" N GLY E 58 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 110 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA E 103 " --> pdb=" O GLN E 18 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLN E 18 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 105 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER E 16 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL E 107 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG E 14 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB8, first strand: chain 'E' and resid 304 through 306 Processing sheet with id=AB9, first strand: chain 'F' and resid 127 through 128 removed outlier: 3.709A pdb=" N ALA F 127 " --> pdb=" O ALA F 32 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.890A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG F 191 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 38 through 39 removed outlier: 5.033A pdb=" N ALA F 272 " --> pdb=" O MET F 44 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 64 through 70 Processing sheet with id=AC4, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AC5, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AC6, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.542A pdb=" N ARG G 117 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG G 191 " --> pdb=" O HIS G 183 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.542A pdb=" N ARG G 117 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 64 through 70 Processing sheet with id=AC9, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AD1, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.868A pdb=" N ALA H 127 " --> pdb=" O ALA H 32 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.987A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG H 191 " --> pdb=" O HIS H 183 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AD4, first strand: chain 'H' and resid 63 through 68 Processing sheet with id=AD5, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AD6, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.630A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.897A pdb=" N ALA I 127 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA I 32 " --> pdb=" O ALA I 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 189 through 196 removed outlier: 3.912A pdb=" N ARG I 191 " --> pdb=" O HIS I 183 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA I 42 " --> pdb=" O ILE I 274 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 274 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA I 272 " --> pdb=" O MET I 44 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 64 through 70 Processing sheet with id=AE1, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AE2, first strand: chain 'J' and resid 17 through 21 Processing sheet with id=AE3, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.541A pdb=" N LEU L 58 " --> pdb=" O ILE L 7 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 100 through 103 removed outlier: 3.803A pdb=" N PHE L 158 " --> pdb=" O VAL L 103 " (cutoff:3.500A) 887 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 8.53 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3968 1.31 - 1.44: 7269 1.44 - 1.56: 13804 1.56 - 1.69: 216 1.69 - 1.81: 39 Bond restraints: 25296 Sorted by residual: bond pdb=" C PRO L 13 " pdb=" O PRO L 13 " ideal model delta sigma weight residual 1.239 1.187 0.052 1.22e-02 6.72e+03 1.82e+01 bond pdb=" N GLN L 35 " pdb=" CA GLN L 35 " ideal model delta sigma weight residual 1.457 1.482 -0.026 6.40e-03 2.44e+04 1.62e+01 bond pdb=" N ILE L 40 " pdb=" CA ILE L 40 " ideal model delta sigma weight residual 1.458 1.501 -0.044 1.14e-02 7.69e+03 1.47e+01 bond pdb=" C PRO A 229 " pdb=" O PRO A 229 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.26e-02 6.30e+03 1.46e+01 bond pdb=" N GLY L 36 " pdb=" CA GLY L 36 " ideal model delta sigma weight residual 1.445 1.476 -0.032 9.90e-03 1.02e+04 1.03e+01 ... (remaining 25291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 34466 3.38 - 6.75: 354 6.75 - 10.13: 38 10.13 - 13.50: 6 13.50 - 16.88: 2 Bond angle restraints: 34866 Sorted by residual: angle pdb=" N ARG L 39 " pdb=" CA ARG L 39 " pdb=" C ARG L 39 " ideal model delta sigma weight residual 111.14 123.18 -12.04 1.08e+00 8.57e-01 1.24e+02 angle pdb=" N PRO L 17 " pdb=" CA PRO L 17 " pdb=" C PRO L 17 " ideal model delta sigma weight residual 112.47 129.35 -16.88 2.06e+00 2.36e-01 6.71e+01 angle pdb=" N TRP C 168 " pdb=" CA TRP C 168 " pdb=" C TRP C 168 " ideal model delta sigma weight residual 111.14 118.89 -7.75 1.08e+00 8.57e-01 5.15e+01 angle pdb=" C PRO L 13 " pdb=" N GLU L 14 " pdb=" CA GLU L 14 " ideal model delta sigma weight residual 120.28 129.18 -8.90 1.34e+00 5.57e-01 4.41e+01 angle pdb=" C GLN L 19 " pdb=" N LEU L 20 " pdb=" CA LEU L 20 " ideal model delta sigma weight residual 120.38 128.89 -8.51 1.37e+00 5.33e-01 3.86e+01 ... (remaining 34861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 14207 35.45 - 70.89: 803 70.89 - 106.34: 64 106.34 - 141.78: 3 141.78 - 177.23: 7 Dihedral angle restraints: 15084 sinusoidal: 6599 harmonic: 8485 Sorted by residual: dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual 232.00 54.77 177.23 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 39 " pdb=" C1' U M 39 " pdb=" N1 U M 39 " pdb=" C2 U M 39 " ideal model delta sinusoidal sigma weight residual -128.00 48.54 -176.54 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C M 37 " pdb=" C1' C M 37 " pdb=" N1 C M 37 " pdb=" C2 C M 37 " ideal model delta sinusoidal sigma weight residual 232.00 61.19 170.81 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 15081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3482 0.073 - 0.147: 448 0.147 - 0.220: 38 0.220 - 0.293: 5 0.293 - 0.366: 2 Chirality restraints: 3975 Sorted by residual: chirality pdb=" CA PRO L 17 " pdb=" N PRO L 17 " pdb=" C PRO L 17 " pdb=" CB PRO L 17 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB ILE F 72 " pdb=" CA ILE F 72 " pdb=" CG1 ILE F 72 " pdb=" CG2 ILE F 72 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA GLN A 225 " pdb=" N GLN A 225 " pdb=" C GLN A 225 " pdb=" CB GLN A 225 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3972 not shown) Planarity restraints: 4196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 14 " 0.022 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C GLU L 14 " -0.079 2.00e-02 2.50e+03 pdb=" O GLU L 14 " 0.029 2.00e-02 2.50e+03 pdb=" N PHE L 15 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 169 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ARG C 169 " -0.071 2.00e-02 2.50e+03 pdb=" O ARG C 169 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN C 170 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 103 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO F 104 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO F 104 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 104 " -0.044 5.00e-02 4.00e+02 ... (remaining 4193 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 668 2.68 - 3.24: 20904 3.24 - 3.79: 39219 3.79 - 4.35: 50429 4.35 - 4.90: 83111 Nonbonded interactions: 194331 Sorted by model distance: nonbonded pdb=" O PRO L 17 " pdb=" N GLN L 19 " model vdw 2.129 3.120 nonbonded pdb=" O GLN L 19 " pdb=" OG SER L 22 " model vdw 2.219 3.040 nonbonded pdb=" O2' C M 50 " pdb=" OP1 U M 52 " model vdw 2.239 3.040 nonbonded pdb=" N ASP L 38 " pdb=" OD1 ASP L 38 " model vdw 2.261 3.120 nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.279 3.040 ... (remaining 194326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 25 through 51 or (resid 52 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 165 or (resid 166 throu \ gh 171 and (name N or name CA or name C or name O or name CB )) or resid 172 thr \ ough 291 or (resid 292 through 294 and (name N or name CA or name C or name O or \ name CB )) or resid 295 through 319 or (resid 320 through 321 and (name N or na \ me CA or name C or name O or name CB )) or resid 322 through 334 or (resid 335 t \ hrough 336 and (name N or name CA or name C or name O or name CB )) or resid 337 \ through 357)) selection = (chain 'D' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 170 or (resid 171 and (name N or name CA or name C or name O or name CB )) or re \ sid 172 through 250 or resid 263 through 317 or (resid 318 and (name N or name C \ A or name C or name O or name CB )) or resid 319 through 334 or (resid 335 throu \ gh 336 and (name N or name CA or name C or name O or name CB )) or resid 337 thr \ ough 357)) selection = (chain 'F' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 165 or (resid 166 through 171 and (name N or name CA or name C or name O or name \ CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 250 or resid 263 through 291 or (res \ id 292 through 294 and (name N or name CA or name C or name O or name CB )) or r \ esid 295 or (resid 296 and (name N or name CA or name C or name O or name CB )) \ or resid 297 through 317 or (resid 318 and (name N or name CA or name C or name \ O or name CB )) or resid 319 or (resid 320 through 321 and (name N or name CA or \ name C or name O or name CB )) or resid 322 through 334 or (resid 335 through 3 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 337 through \ 357)) selection = (chain 'G' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or re \ sid 204 through 250 or resid 263 through 290 or (resid 291 through 294 and (name \ N or name CA or name C or name O or name CB )) or resid 295 through 317 or (res \ id 318 and (name N or name CA or name C or name O or name CB )) or resid 319 or \ (resid 320 through 321 and (name N or name CA or name C or name O or name CB )) \ or resid 322 through 334 or (resid 335 through 336 and (name N or name CA or nam \ e C or name O or name CB )) or resid 337 through 357)) selection = (chain 'H' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 166 or (resid 167 through 171 and (name N or name CA or name C or name O or name \ CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 250 or resid 263 through 295 or (res \ id 296 and (name N or name CA or name C or name O or name CB )) or resid 297 thr \ ough 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) \ or resid 319 or (resid 320 through 321 and (name N or name CA or name C or name \ O or name CB )) or resid 322 through 334 or (resid 335 through 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 through 357)) selection = (chain 'I' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 165 or (resid 166 through 171 and (name N or name CA or name C or name O or name \ CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 250 or resid 263 through 291 or (res \ id 292 through 294 and (name N or name CA or name C or name O or name CB )) or r \ esid 295 through 317 or (resid 318 and (name N or name CA or name C or name O or \ name CB )) or resid 319 or (resid 320 through 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 357)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 60.810 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25296 Z= 0.251 Angle : 0.908 16.880 34866 Z= 0.517 Chirality : 0.050 0.366 3975 Planarity : 0.007 0.081 4196 Dihedral : 20.462 177.230 9602 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.96 % Favored : 91.97 % Rotamer: Outliers : 7.08 % Allowed : 17.46 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.12), residues: 2915 helix: -2.92 (0.12), residues: 837 sheet: -0.84 (0.24), residues: 432 loop : -3.51 (0.11), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 228 HIS 0.006 0.001 HIS G 343 PHE 0.019 0.002 PHE C 235 TYR 0.021 0.002 TYR G 290 ARG 0.011 0.001 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.13917 ( 940) hydrogen bonds : angle 6.47852 ( 2647) covalent geometry : bond 0.00493 (25296) covalent geometry : angle 0.90803 (34866) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 322 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7240 (tp) REVERT: A 156 ARG cc_start: 0.6210 (tmt170) cc_final: 0.5109 (tpt170) REVERT: A 193 LEU cc_start: 0.7991 (mt) cc_final: 0.7781 (mt) REVERT: A 390 ARG cc_start: 0.6708 (ttm170) cc_final: 0.6479 (ttm110) REVERT: C 117 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6287 (ptt180) REVERT: C 283 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6310 (mp) REVERT: C 333 ARG cc_start: 0.2880 (OUTLIER) cc_final: 0.2627 (mtm180) REVERT: D 198 LEU cc_start: 0.2158 (OUTLIER) cc_final: 0.1957 (mt) REVERT: E 124 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6623 (pp30) REVERT: E 133 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7362 (tm-30) REVERT: E 138 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7085 (mtt90) REVERT: F 113 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6887 (ttt90) REVERT: G 31 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6614 (tt) REVERT: G 91 GLN cc_start: 0.5825 (OUTLIER) cc_final: 0.5570 (mt0) REVERT: H 117 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7657 (ttm170) REVERT: H 138 LEU cc_start: 0.8000 (mt) cc_final: 0.7774 (mp) REVERT: H 285 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7581 (m) REVERT: L 24 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6494 (tp) REVERT: L 40 ILE cc_start: 0.6289 (OUTLIER) cc_final: 0.5967 (pt) REVERT: L 102 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.5079 (ppt90) outliers start: 154 outliers final: 93 residues processed: 447 average time/residue: 0.4241 time to fit residues: 284.9927 Evaluate side-chains 408 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 300 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 17 PRO Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 102 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 6.9990 chunk 226 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 174 optimal weight: 0.0470 chunk 271 optimal weight: 9.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 241 GLN A 271 HIS A 283 HIS A 305 GLN C 159 HIS C 183 HIS C 186 GLN C 275 HIS C 277 GLN C 341 GLN C 348 ASN D 186 GLN E 82 ASN E 129 GLN E 194 GLN E 195 GLN F 91 GLN F 102 ASN F 170 ASN F 281 ASN F 316 GLN F 319 GLN G 56 GLN G 94 ASN G 159 HIS H 129 ASN H 329 ASN I 91 GLN I 102 ASN J 27 GLN ** L 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 HIS L 104 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.184734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.163081 restraints weight = 35875.722| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.54 r_work: 0.3873 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25296 Z= 0.157 Angle : 0.612 14.173 34866 Z= 0.325 Chirality : 0.041 0.209 3975 Planarity : 0.005 0.065 4196 Dihedral : 19.801 176.092 4889 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.75 % Favored : 92.21 % Rotamer: Outliers : 5.06 % Allowed : 20.77 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.13), residues: 2915 helix: -1.07 (0.16), residues: 838 sheet: -0.48 (0.25), residues: 450 loop : -3.09 (0.12), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 193 HIS 0.011 0.001 HIS E 114 PHE 0.021 0.002 PHE C 323 TYR 0.017 0.002 TYR C 144 ARG 0.007 0.001 ARG E 315 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 940) hydrogen bonds : angle 4.80009 ( 2647) covalent geometry : bond 0.00347 (25296) covalent geometry : angle 0.61156 (34866) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 302 time to evaluate : 2.489 Fit side-chains revert: symmetry clash REVERT: A 53 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6217 (tt) REVERT: A 63 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7366 (tp) REVERT: A 99 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 105 VAL cc_start: 0.6406 (OUTLIER) cc_final: 0.5688 (t) REVERT: A 156 ARG cc_start: 0.6453 (tmt170) cc_final: 0.4905 (tpt170) REVERT: A 235 TYR cc_start: 0.7603 (m-80) cc_final: 0.7173 (m-80) REVERT: A 390 ARG cc_start: 0.7627 (ttm170) cc_final: 0.7126 (mtp-110) REVERT: C 112 VAL cc_start: 0.5413 (OUTLIER) cc_final: 0.5122 (t) REVERT: C 186 GLN cc_start: 0.5940 (OUTLIER) cc_final: 0.5632 (pm20) REVERT: E 133 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7621 (tm-30) REVERT: E 138 ARG cc_start: 0.7616 (ptp-170) cc_final: 0.7230 (mtt90) REVERT: F 113 ARG cc_start: 0.7736 (ttt90) cc_final: 0.7393 (ttt90) REVERT: F 289 TRP cc_start: 0.8061 (m-90) cc_final: 0.7812 (m-90) REVERT: G 31 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6835 (tt) REVERT: H 110 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7722 (tp) REVERT: H 117 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7754 (ttm170) REVERT: L 24 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6903 (tp) REVERT: L 83 LEU cc_start: 0.6317 (mt) cc_final: 0.6069 (mt) REVERT: L 117 MET cc_start: 0.6620 (mmm) cc_final: 0.6159 (mmm) REVERT: L 118 ARG cc_start: 0.7908 (tpm170) cc_final: 0.7169 (tpm170) outliers start: 110 outliers final: 66 residues processed: 391 average time/residue: 0.4187 time to fit residues: 243.7770 Evaluate side-chains 368 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 292 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 77 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 271 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 27 optimal weight: 0.0570 chunk 177 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS C 170 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 GLN E 293 HIS G 94 ASN G 129 ASN G 343 HIS I 102 ASN I 227 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.180201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.157918 restraints weight = 35659.610| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.70 r_work: 0.3809 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 25296 Z= 0.306 Angle : 0.739 12.968 34866 Z= 0.388 Chirality : 0.047 0.251 3975 Planarity : 0.006 0.072 4196 Dihedral : 19.859 177.353 4780 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.85 % Favored : 90.12 % Rotamer: Outliers : 7.08 % Allowed : 21.28 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.14), residues: 2915 helix: -0.71 (0.16), residues: 840 sheet: -0.41 (0.25), residues: 454 loop : -3.03 (0.13), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 49 HIS 0.009 0.002 HIS E 114 PHE 0.036 0.003 PHE D 245 TYR 0.029 0.003 TYR D 266 ARG 0.008 0.001 ARG I 315 Details of bonding type rmsd hydrogen bonds : bond 0.05304 ( 940) hydrogen bonds : angle 5.02586 ( 2647) covalent geometry : bond 0.00693 (25296) covalent geometry : angle 0.73924 (34866) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 310 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6366 (tt) REVERT: A 105 VAL cc_start: 0.6483 (OUTLIER) cc_final: 0.5814 (t) REVERT: A 156 ARG cc_start: 0.6553 (tmt170) cc_final: 0.4943 (tpt170) REVERT: A 235 TYR cc_start: 0.7715 (m-80) cc_final: 0.7411 (m-80) REVERT: A 305 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7190 (mp10) REVERT: A 361 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5550 (tt) REVERT: A 390 ARG cc_start: 0.7625 (ttm170) cc_final: 0.7061 (mtp-110) REVERT: E 133 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7648 (tm-30) REVERT: E 138 ARG cc_start: 0.7732 (ptp-170) cc_final: 0.7323 (mtt90) REVERT: E 242 ARG cc_start: 0.6967 (mmm160) cc_final: 0.6691 (mmm160) REVERT: F 25 LEU cc_start: 0.4690 (OUTLIER) cc_final: 0.4469 (tt) REVERT: F 113 ARG cc_start: 0.7729 (ttt90) cc_final: 0.7456 (ttt90) REVERT: G 31 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6783 (tt) REVERT: H 110 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7866 (tp) REVERT: H 117 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7594 (ttm170) REVERT: H 155 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7539 (ttp80) REVERT: I 249 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: L 24 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6964 (tp) REVERT: L 83 LEU cc_start: 0.6579 (mt) cc_final: 0.6338 (mt) REVERT: L 117 MET cc_start: 0.6539 (mmm) cc_final: 0.6094 (mmm) REVERT: L 118 ARG cc_start: 0.8017 (tpm170) cc_final: 0.7314 (tpm170) outliers start: 154 outliers final: 103 residues processed: 429 average time/residue: 0.4136 time to fit residues: 266.3715 Evaluate side-chains 412 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 299 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 289 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 187 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN C 186 GLN E 168 GLN E 282 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 342 GLN I 102 ASN L 19 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.184133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.163124 restraints weight = 36067.768| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.54 r_work: 0.3872 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25296 Z= 0.137 Angle : 0.587 12.878 34866 Z= 0.310 Chirality : 0.040 0.208 3975 Planarity : 0.005 0.063 4196 Dihedral : 19.495 177.119 4778 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.20 % Favored : 92.76 % Rotamer: Outliers : 6.16 % Allowed : 22.52 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 2915 helix: 0.00 (0.17), residues: 841 sheet: -0.15 (0.25), residues: 453 loop : -2.82 (0.13), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 330 HIS 0.009 0.001 HIS E 114 PHE 0.013 0.001 PHE D 245 TYR 0.022 0.002 TYR I 144 ARG 0.005 0.000 ARG I 315 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 940) hydrogen bonds : angle 4.47597 ( 2647) covalent geometry : bond 0.00299 (25296) covalent geometry : angle 0.58734 (34866) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 303 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5788 (mp) REVERT: A 53 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6323 (tt) REVERT: A 63 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7317 (tp) REVERT: A 65 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6423 (mm) REVERT: A 105 VAL cc_start: 0.6394 (OUTLIER) cc_final: 0.5745 (t) REVERT: A 156 ARG cc_start: 0.6449 (tmt170) cc_final: 0.4890 (tpt170) REVERT: A 235 TYR cc_start: 0.7623 (m-80) cc_final: 0.7222 (m-80) REVERT: A 305 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: C 333 ARG cc_start: 0.3331 (OUTLIER) cc_final: 0.2918 (mtm180) REVERT: E 128 ARG cc_start: 0.7368 (ttp-110) cc_final: 0.7163 (ttp80) REVERT: E 133 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7681 (tm-30) REVERT: E 138 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7189 (mtt90) REVERT: E 242 ARG cc_start: 0.6770 (mmm160) cc_final: 0.6556 (mmm160) REVERT: F 35 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.5979 (ttp-170) REVERT: F 113 ARG cc_start: 0.7741 (ttt90) cc_final: 0.7389 (ttt90) REVERT: G 31 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6640 (tt) REVERT: G 229 LEU cc_start: 0.7513 (tp) cc_final: 0.7264 (tp) REVERT: G 237 ARG cc_start: 0.7158 (ttt180) cc_final: 0.6946 (ttt180) REVERT: G 265 LEU cc_start: 0.8674 (mt) cc_final: 0.8425 (mp) REVERT: H 43 LEU cc_start: 0.7616 (mm) cc_final: 0.7389 (mt) REVERT: H 110 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7744 (tp) REVERT: H 117 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7667 (ttm170) REVERT: H 130 ASP cc_start: 0.6537 (t70) cc_final: 0.6306 (t70) REVERT: L 1 MET cc_start: 0.2925 (mmm) cc_final: 0.2245 (mmm) REVERT: L 24 LEU cc_start: 0.7341 (tp) cc_final: 0.7095 (tt) REVERT: L 83 LEU cc_start: 0.6542 (mt) cc_final: 0.6327 (mt) REVERT: L 117 MET cc_start: 0.6340 (mmm) cc_final: 0.5789 (mmm) REVERT: L 118 ARG cc_start: 0.7924 (tpm170) cc_final: 0.7294 (tpm170) outliers start: 134 outliers final: 89 residues processed: 409 average time/residue: 0.4173 time to fit residues: 256.7917 Evaluate side-chains 397 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 296 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 160 optimal weight: 0.7980 chunk 259 optimal weight: 0.7980 chunk 2 optimal weight: 0.0970 chunk 181 optimal weight: 2.9990 chunk 298 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 228 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN C 186 GLN C 348 ASN E 282 ASN G 94 ASN I 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.183780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.161920 restraints weight = 35991.663| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.61 r_work: 0.3864 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25296 Z= 0.157 Angle : 0.595 12.192 34866 Z= 0.313 Chirality : 0.041 0.240 3975 Planarity : 0.005 0.052 4196 Dihedral : 19.429 176.780 4774 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.58 % Favored : 91.39 % Rotamer: Outliers : 6.76 % Allowed : 23.48 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.15), residues: 2915 helix: 0.26 (0.17), residues: 848 sheet: -0.04 (0.25), residues: 451 loop : -2.75 (0.14), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 330 HIS 0.009 0.001 HIS E 114 PHE 0.019 0.002 PHE D 245 TYR 0.022 0.002 TYR I 144 ARG 0.005 0.000 ARG F 171 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 940) hydrogen bonds : angle 4.42132 ( 2647) covalent geometry : bond 0.00350 (25296) covalent geometry : angle 0.59519 (34866) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 304 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5730 (mp) REVERT: A 53 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6336 (tt) REVERT: A 63 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7324 (tp) REVERT: A 65 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6471 (mm) REVERT: A 156 ARG cc_start: 0.6502 (tmt170) cc_final: 0.4932 (tpt170) REVERT: A 235 TYR cc_start: 0.7621 (m-80) cc_final: 0.7216 (m-80) REVERT: A 305 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: A 339 ARG cc_start: 0.6778 (ttm110) cc_final: 0.6415 (ttm110) REVERT: A 361 LEU cc_start: 0.5605 (OUTLIER) cc_final: 0.5373 (tt) REVERT: A 386 GLU cc_start: 0.6452 (pp20) cc_final: 0.6128 (pp20) REVERT: C 333 ARG cc_start: 0.3428 (OUTLIER) cc_final: 0.2860 (mtm180) REVERT: E 128 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.7094 (ttp80) REVERT: E 133 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7721 (tm-30) REVERT: E 138 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7225 (mtt90) REVERT: E 242 ARG cc_start: 0.6780 (mmm160) cc_final: 0.6495 (mmm160) REVERT: F 113 ARG cc_start: 0.7753 (ttt90) cc_final: 0.7440 (ttt90) REVERT: G 31 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6656 (tt) REVERT: G 265 LEU cc_start: 0.8725 (mt) cc_final: 0.8474 (mp) REVERT: H 110 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7828 (tp) REVERT: H 130 ASP cc_start: 0.6539 (t70) cc_final: 0.6315 (t70) REVERT: I 249 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6458 (mp0) REVERT: L 24 LEU cc_start: 0.7350 (tp) cc_final: 0.7111 (tt) REVERT: L 83 LEU cc_start: 0.6657 (mt) cc_final: 0.6419 (mt) REVERT: L 117 MET cc_start: 0.6233 (mmm) cc_final: 0.5742 (mmm) REVERT: L 118 ARG cc_start: 0.7844 (tpm170) cc_final: 0.7118 (tpm170) outliers start: 147 outliers final: 107 residues processed: 414 average time/residue: 0.4454 time to fit residues: 276.7673 Evaluate side-chains 417 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 299 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 29 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 198 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 293 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN C 275 HIS E 282 ASN G 94 ASN I 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.185252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.163472 restraints weight = 35933.428| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.59 r_work: 0.3888 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25296 Z= 0.123 Angle : 0.565 13.004 34866 Z= 0.297 Chirality : 0.040 0.225 3975 Planarity : 0.004 0.045 4196 Dihedral : 19.266 176.966 4771 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.20 % Favored : 92.76 % Rotamer: Outliers : 6.25 % Allowed : 23.48 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.15), residues: 2915 helix: 0.56 (0.18), residues: 850 sheet: 0.20 (0.25), residues: 450 loop : -2.66 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 289 HIS 0.010 0.001 HIS E 114 PHE 0.015 0.001 PHE F 245 TYR 0.023 0.002 TYR I 144 ARG 0.007 0.000 ARG E 315 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 940) hydrogen bonds : angle 4.23424 ( 2647) covalent geometry : bond 0.00267 (25296) covalent geometry : angle 0.56498 (34866) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 300 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.5079 (OUTLIER) cc_final: 0.4682 (mp) REVERT: A 25 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5736 (mp) REVERT: A 63 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7308 (tp) REVERT: A 65 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6395 (mm) REVERT: A 156 ARG cc_start: 0.6494 (tmt170) cc_final: 0.4942 (tpt170) REVERT: A 226 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: A 235 TYR cc_start: 0.7596 (m-80) cc_final: 0.7117 (m-80) REVERT: A 305 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7141 (mp10) REVERT: A 339 ARG cc_start: 0.6795 (ttm110) cc_final: 0.6442 (ttm110) REVERT: A 361 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5308 (tt) REVERT: A 390 ARG cc_start: 0.7587 (ttm170) cc_final: 0.7097 (mtp-110) REVERT: C 44 MET cc_start: 0.6117 (ppp) cc_final: 0.5831 (ppp) REVERT: C 112 VAL cc_start: 0.5264 (OUTLIER) cc_final: 0.4972 (t) REVERT: C 333 ARG cc_start: 0.3498 (OUTLIER) cc_final: 0.3097 (mtm180) REVERT: E 128 ARG cc_start: 0.7361 (ttp-110) cc_final: 0.7088 (ttp80) REVERT: E 133 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7720 (tm-30) REVERT: E 138 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7057 (mtt-85) REVERT: E 156 ASN cc_start: 0.6937 (OUTLIER) cc_final: 0.6613 (t0) REVERT: F 35 ARG cc_start: 0.6402 (OUTLIER) cc_final: 0.5998 (ttp-170) REVERT: F 113 ARG cc_start: 0.7718 (ttt90) cc_final: 0.7393 (ttt90) REVERT: F 168 TRP cc_start: 0.7318 (m100) cc_final: 0.6969 (m100) REVERT: G 31 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6715 (tt) REVERT: H 130 ASP cc_start: 0.6563 (t70) cc_final: 0.6315 (t0) REVERT: I 249 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: I 290 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.6384 (p90) REVERT: L 1 MET cc_start: 0.3311 (mmm) cc_final: 0.2647 (mmm) REVERT: L 83 LEU cc_start: 0.6623 (mt) cc_final: 0.6395 (mt) REVERT: L 114 ARG cc_start: 0.5989 (ptm160) cc_final: 0.5350 (ttp-170) REVERT: L 117 MET cc_start: 0.6009 (mmm) cc_final: 0.5599 (mmm) REVERT: L 118 ARG cc_start: 0.7798 (tpm170) cc_final: 0.7067 (tpm170) outliers start: 136 outliers final: 100 residues processed: 410 average time/residue: 0.4080 time to fit residues: 250.8093 Evaluate side-chains 410 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 295 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 289 TRP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 290 TYR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 212 optimal weight: 0.0030 chunk 121 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 190 optimal weight: 0.0980 chunk 195 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 182 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN E 282 ASN F 170 ASN I 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.186141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.164314 restraints weight = 36136.076| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.59 r_work: 0.3893 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25296 Z= 0.116 Angle : 0.556 12.686 34866 Z= 0.291 Chirality : 0.039 0.232 3975 Planarity : 0.004 0.051 4196 Dihedral : 19.176 177.097 4762 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.31 % Favored : 92.66 % Rotamer: Outliers : 6.25 % Allowed : 24.13 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 2915 helix: 0.73 (0.18), residues: 859 sheet: 0.29 (0.25), residues: 452 loop : -2.59 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 289 HIS 0.010 0.001 HIS E 114 PHE 0.011 0.001 PHE F 166 TYR 0.024 0.001 TYR I 144 ARG 0.012 0.000 ARG H 194 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 940) hydrogen bonds : angle 4.12283 ( 2647) covalent geometry : bond 0.00250 (25296) covalent geometry : angle 0.55604 (34866) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 292 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.5070 (OUTLIER) cc_final: 0.4681 (mp) REVERT: A 25 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5747 (mp) REVERT: A 63 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7302 (tp) REVERT: A 65 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6420 (mm) REVERT: A 105 VAL cc_start: 0.6254 (OUTLIER) cc_final: 0.5560 (t) REVERT: A 156 ARG cc_start: 0.6506 (tmt170) cc_final: 0.4928 (tpt170) REVERT: A 235 TYR cc_start: 0.7584 (m-80) cc_final: 0.7114 (m-80) REVERT: A 305 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: A 361 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.5294 (tt) REVERT: C 44 MET cc_start: 0.6103 (ppp) cc_final: 0.5817 (ppp) REVERT: C 112 VAL cc_start: 0.5189 (OUTLIER) cc_final: 0.4905 (t) REVERT: E 133 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7751 (tm-30) REVERT: E 138 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7080 (mtt90) REVERT: E 156 ASN cc_start: 0.6937 (OUTLIER) cc_final: 0.6601 (t0) REVERT: F 35 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.6070 (ptp90) REVERT: F 113 ARG cc_start: 0.7675 (ttt90) cc_final: 0.7378 (ttt90) REVERT: F 168 TRP cc_start: 0.7309 (m100) cc_final: 0.6996 (m100) REVERT: G 31 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6680 (tt) REVERT: G 307 VAL cc_start: 0.6502 (OUTLIER) cc_final: 0.6263 (t) REVERT: H 130 ASP cc_start: 0.6562 (t70) cc_final: 0.6316 (t0) REVERT: I 249 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: I 290 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.6277 (p90) REVERT: L 1 MET cc_start: 0.3151 (mmm) cc_final: 0.2747 (mmm) REVERT: L 83 LEU cc_start: 0.6557 (mt) cc_final: 0.6318 (mt) REVERT: L 114 ARG cc_start: 0.6079 (ptm160) cc_final: 0.5049 (ttp-110) REVERT: L 117 MET cc_start: 0.6061 (mmm) cc_final: 0.5631 (mmm) REVERT: L 118 ARG cc_start: 0.7782 (tpm170) cc_final: 0.7130 (tpm170) outliers start: 136 outliers final: 105 residues processed: 403 average time/residue: 0.4477 time to fit residues: 272.0854 Evaluate side-chains 411 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 291 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 289 TRP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 309 SER Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 290 TYR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 81 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 75 optimal weight: 0.0870 chunk 243 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 278 optimal weight: 0.6980 chunk 268 optimal weight: 9.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN E 282 ASN F 170 ASN I 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.185326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.163263 restraints weight = 36029.918| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.60 r_work: 0.3887 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25296 Z= 0.140 Angle : 0.574 12.290 34866 Z= 0.300 Chirality : 0.040 0.246 3975 Planarity : 0.004 0.055 4196 Dihedral : 19.154 176.950 4757 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.13 % Favored : 91.84 % Rotamer: Outliers : 6.39 % Allowed : 23.90 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 2915 helix: 0.73 (0.18), residues: 860 sheet: 0.33 (0.25), residues: 450 loop : -2.56 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 289 HIS 0.010 0.001 HIS E 114 PHE 0.016 0.002 PHE L 44 TYR 0.022 0.002 TYR I 144 ARG 0.013 0.000 ARG H 194 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 940) hydrogen bonds : angle 4.16537 ( 2647) covalent geometry : bond 0.00313 (25296) covalent geometry : angle 0.57362 (34866) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 293 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.5063 (OUTLIER) cc_final: 0.4699 (mp) REVERT: A 25 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5729 (mp) REVERT: A 63 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7343 (tp) REVERT: A 65 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6421 (mm) REVERT: A 105 VAL cc_start: 0.6217 (OUTLIER) cc_final: 0.5521 (t) REVERT: A 108 VAL cc_start: 0.6051 (OUTLIER) cc_final: 0.5835 (t) REVERT: A 226 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: A 235 TYR cc_start: 0.7556 (m-80) cc_final: 0.7088 (m-80) REVERT: A 305 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7132 (mp10) REVERT: A 361 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.5219 (tt) REVERT: A 390 ARG cc_start: 0.7571 (ttm170) cc_final: 0.7106 (mtp-110) REVERT: C 112 VAL cc_start: 0.5197 (OUTLIER) cc_final: 0.4912 (t) REVERT: C 333 ARG cc_start: 0.3527 (OUTLIER) cc_final: 0.3157 (mtm180) REVERT: E 133 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7606 (tm-30) REVERT: E 138 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7133 (mtt90) REVERT: E 156 ASN cc_start: 0.6931 (OUTLIER) cc_final: 0.6627 (t0) REVERT: E 158 GLU cc_start: 0.5441 (OUTLIER) cc_final: 0.4930 (tp30) REVERT: F 35 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5844 (ptp-110) REVERT: F 113 ARG cc_start: 0.7750 (ttt90) cc_final: 0.7449 (ttt90) REVERT: F 168 TRP cc_start: 0.7341 (m100) cc_final: 0.7011 (m100) REVERT: G 31 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6714 (tt) REVERT: H 130 ASP cc_start: 0.6595 (t70) cc_final: 0.6366 (t0) REVERT: I 249 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6445 (mp0) REVERT: I 265 LEU cc_start: 0.8048 (mt) cc_final: 0.7673 (tp) REVERT: I 290 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.6296 (p90) REVERT: I 357 GLU cc_start: 0.5654 (mp0) cc_final: 0.5252 (mp0) REVERT: L 1 MET cc_start: 0.3033 (mmm) cc_final: 0.2777 (mmm) REVERT: L 83 LEU cc_start: 0.6596 (mt) cc_final: 0.6359 (mt) REVERT: L 114 ARG cc_start: 0.6021 (ptm160) cc_final: 0.5513 (ttp-170) REVERT: L 117 MET cc_start: 0.5992 (mmm) cc_final: 0.5610 (mmm) REVERT: L 118 ARG cc_start: 0.7759 (tpm170) cc_final: 0.7072 (tpm170) outliers start: 139 outliers final: 109 residues processed: 406 average time/residue: 0.5119 time to fit residues: 313.9075 Evaluate side-chains 417 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 290 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 289 TRP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 309 SER Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 290 TYR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 246 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 150 optimal weight: 0.3980 chunk 255 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 292 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 96 optimal weight: 0.4980 chunk 241 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN C 186 GLN C 227 HIS E 282 ASN F 170 ASN I 102 ASN J 40 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.186823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.164647 restraints weight = 36184.521| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 1.60 r_work: 0.3916 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25296 Z= 0.111 Angle : 0.554 11.702 34866 Z= 0.288 Chirality : 0.039 0.241 3975 Planarity : 0.004 0.060 4196 Dihedral : 19.059 177.179 4757 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.31 % Favored : 92.66 % Rotamer: Outliers : 5.97 % Allowed : 24.17 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.15), residues: 2915 helix: 0.94 (0.18), residues: 858 sheet: 0.32 (0.25), residues: 462 loop : -2.49 (0.14), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 289 HIS 0.011 0.001 HIS E 114 PHE 0.017 0.001 PHE L 44 TYR 0.023 0.001 TYR I 144 ARG 0.013 0.000 ARG H 194 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 940) hydrogen bonds : angle 4.04195 ( 2647) covalent geometry : bond 0.00240 (25296) covalent geometry : angle 0.55394 (34866) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 282 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.4940 (OUTLIER) cc_final: 0.4576 (mp) REVERT: A 25 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5723 (mp) REVERT: A 63 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7298 (tp) REVERT: A 65 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6386 (mm) REVERT: A 105 VAL cc_start: 0.6159 (OUTLIER) cc_final: 0.5454 (t) REVERT: A 226 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: A 235 TYR cc_start: 0.7500 (m-80) cc_final: 0.7023 (m-80) REVERT: A 305 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.7090 (mp10) REVERT: A 361 LEU cc_start: 0.5396 (OUTLIER) cc_final: 0.5180 (tt) REVERT: C 112 VAL cc_start: 0.5231 (OUTLIER) cc_final: 0.4944 (t) REVERT: C 333 ARG cc_start: 0.3575 (OUTLIER) cc_final: 0.3230 (mtm180) REVERT: E 138 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7087 (mtt90) REVERT: E 156 ASN cc_start: 0.6902 (OUTLIER) cc_final: 0.6600 (t0) REVERT: E 158 GLU cc_start: 0.5390 (OUTLIER) cc_final: 0.4905 (tp30) REVERT: F 35 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6037 (ptp90) REVERT: F 113 ARG cc_start: 0.7709 (ttt90) cc_final: 0.7400 (ttt90) REVERT: F 168 TRP cc_start: 0.7303 (m100) cc_final: 0.6999 (m100) REVERT: G 31 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6683 (tt) REVERT: G 307 VAL cc_start: 0.6593 (OUTLIER) cc_final: 0.6354 (t) REVERT: H 34 GLU cc_start: 0.7041 (tp30) cc_final: 0.6832 (tp30) REVERT: H 130 ASP cc_start: 0.6542 (t70) cc_final: 0.6299 (t0) REVERT: I 169 ARG cc_start: 0.6580 (ttp80) cc_final: 0.6053 (ttt180) REVERT: I 249 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6393 (mp0) REVERT: I 265 LEU cc_start: 0.8053 (mt) cc_final: 0.7641 (tp) REVERT: L 83 LEU cc_start: 0.6554 (mt) cc_final: 0.6303 (mt) REVERT: L 117 MET cc_start: 0.5989 (mmm) cc_final: 0.5544 (mmm) REVERT: L 118 ARG cc_start: 0.7717 (tpm170) cc_final: 0.6992 (tpm170) outliers start: 130 outliers final: 102 residues processed: 389 average time/residue: 0.4273 time to fit residues: 248.9969 Evaluate side-chains 399 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 280 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 289 TRP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 309 SER Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 60 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 64 optimal weight: 0.0270 chunk 23 optimal weight: 0.0040 chunk 212 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 overall best weight: 0.5652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN E 64 HIS E 282 ASN F 170 ASN I 102 ASN L 154 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.189403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.167192 restraints weight = 35976.101| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.61 r_work: 0.3922 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25296 Z= 0.109 Angle : 0.552 11.310 34866 Z= 0.286 Chirality : 0.039 0.250 3975 Planarity : 0.004 0.064 4196 Dihedral : 18.984 177.183 4751 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.24 % Favored : 92.73 % Rotamer: Outliers : 5.70 % Allowed : 24.72 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 2915 helix: 1.08 (0.18), residues: 858 sheet: 0.40 (0.25), residues: 458 loop : -2.48 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 289 HIS 0.011 0.001 HIS E 114 PHE 0.016 0.001 PHE L 44 TYR 0.022 0.001 TYR I 144 ARG 0.014 0.000 ARG H 194 Details of bonding type rmsd hydrogen bonds : bond 0.03122 ( 940) hydrogen bonds : angle 4.00363 ( 2647) covalent geometry : bond 0.00236 (25296) covalent geometry : angle 0.55242 (34866) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 282 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.4927 (OUTLIER) cc_final: 0.4566 (mp) REVERT: A 25 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5723 (mp) REVERT: A 63 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7318 (tp) REVERT: A 65 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6359 (mm) REVERT: A 105 VAL cc_start: 0.6125 (OUTLIER) cc_final: 0.5417 (t) REVERT: A 156 ARG cc_start: 0.6539 (tmt170) cc_final: 0.5095 (tpp80) REVERT: A 226 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7232 (mt-10) REVERT: A 235 TYR cc_start: 0.7522 (m-80) cc_final: 0.7042 (m-80) REVERT: A 285 SER cc_start: 0.6375 (t) cc_final: 0.5990 (p) REVERT: A 305 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7111 (mp10) REVERT: A 361 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.5171 (tt) REVERT: C 112 VAL cc_start: 0.5186 (OUTLIER) cc_final: 0.4904 (t) REVERT: C 333 ARG cc_start: 0.3570 (OUTLIER) cc_final: 0.3166 (mtm180) REVERT: E 138 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7115 (mtt90) REVERT: E 156 ASN cc_start: 0.6883 (OUTLIER) cc_final: 0.6578 (t0) REVERT: E 158 GLU cc_start: 0.5424 (OUTLIER) cc_final: 0.4957 (tp30) REVERT: F 35 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6024 (ptp90) REVERT: F 113 ARG cc_start: 0.7649 (ttt90) cc_final: 0.7351 (ttt90) REVERT: F 168 TRP cc_start: 0.7329 (m100) cc_final: 0.7021 (m100) REVERT: G 31 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6732 (tt) REVERT: G 307 VAL cc_start: 0.6600 (OUTLIER) cc_final: 0.6364 (t) REVERT: H 34 GLU cc_start: 0.7042 (tp30) cc_final: 0.6808 (tp30) REVERT: H 130 ASP cc_start: 0.6585 (t70) cc_final: 0.6341 (t0) REVERT: I 249 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: I 265 LEU cc_start: 0.8042 (mt) cc_final: 0.7638 (tp) REVERT: L 83 LEU cc_start: 0.6556 (mt) cc_final: 0.6225 (mt) REVERT: L 113 ARG cc_start: 0.6338 (ptp90) cc_final: 0.5696 (ttm110) REVERT: L 117 MET cc_start: 0.6013 (mmm) cc_final: 0.5532 (mmm) outliers start: 124 outliers final: 101 residues processed: 383 average time/residue: 0.4354 time to fit residues: 249.4476 Evaluate side-chains 397 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 279 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 309 SER Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 38 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 285 optimal weight: 0.8980 chunk 190 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 0.0980 chunk 120 optimal weight: 0.5980 chunk 235 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN E 282 ASN F 129 ASN F 170 ASN H 310 GLN I 102 ASN L 154 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.187778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.165028 restraints weight = 35991.548| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.74 r_work: 0.3921 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25296 Z= 0.110 Angle : 0.551 11.661 34866 Z= 0.285 Chirality : 0.039 0.247 3975 Planarity : 0.004 0.060 4196 Dihedral : 18.916 177.103 4750 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.07 % Favored : 92.90 % Rotamer: Outliers : 5.51 % Allowed : 24.95 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 2915 helix: 1.15 (0.18), residues: 858 sheet: 0.44 (0.25), residues: 458 loop : -2.45 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 289 HIS 0.010 0.001 HIS E 114 PHE 0.012 0.001 PHE L 44 TYR 0.022 0.001 TYR I 144 ARG 0.013 0.000 ARG H 194 Details of bonding type rmsd hydrogen bonds : bond 0.03085 ( 940) hydrogen bonds : angle 3.97042 ( 2647) covalent geometry : bond 0.00239 (25296) covalent geometry : angle 0.55098 (34866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15885.39 seconds wall clock time: 280 minutes 14.28 seconds (16814.28 seconds total)